This invention is in the field of plant molecular biology. More specifically, this invention pertains to nucleic acid fragments encoding metabolism proteins in plants and seeds.
Gibberellic acid (GA) is an important regulator (phytohormone) of plant development. Gibberellic acid has been shown to stimulate elongation in the internodes of stems and to play roles in flower and fruit development. Identification and characterization of genes involved in GA biosynthesis will permit genetic engineering methods aimed at modulating levels of GA in plants which will in turn allow for better control of plant stature, fertility and plant development in general (see World Patent Publication No. WO 95/35383).
Gibberellic acid is synthesized from isoprenoid geranylgeranyl diphosphate (GGDP), beginning with the conversion of GGDP to copalyl diphosphate (CDP). Copalyl diphosphate is then converted to GA12-aldehyde which in turn can be converted to a number of different gibberellins required for normal plant development. For example GA-20 oxidase catalizes the conversion of GA12 to GA9. A key enzyme in the synthesis of gibberellin is dioxygenase which appears to play a role in the conversion of GA12-aldehyde to GA9 and GA25. Because GA12-aldehyde dioxygenase appears to catalyze key steps in the synthesis of GA it is a target enzymes that may be manipulated to control GA levels. Ent-Kaurene synthase A (KSA) catalyzes the conversion of GGDP to CDP, which is subsequently converted to ent-kaurene by ent-kaurene synthase B (KSB) (Yamaguchi et al. (1996) Plant J. 10(2):203-213). Gibberillin 3-beta-hydroxylase catalizes the conversion of GA20 to GA1 a major gibberellin that is involved in controlling stem elongation. These enzymes catalyze key steps in the synthesis of GA and thus provide target enzymes that may be manipulated to control GA levels.
Thus there is a great deal of interest in identifying genes that encode proteins that may be used to control plant developmental. Accordingly, the availability of nucleic acid sequences encoding all or a substantial portion of a GA dioxygenase would facilitate studies to better understand plant development and provide tools to genetically engineer improved developmental properties in plants.
Riboflavin is the precursor to essential electron transport chain components and redox coenzymes such as flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Humans, unlike plants and bacteria, are incapable of synthesizing riboflavin (vitamin B2) from GTP, and must obtain this compound through their diet. Thousands of tons of riboflavin are produced each year as additives for food and animal feed (Bacher et al. (1997) Methods Enzymol 280:382-389). Historically, riboflavin has been made via chemical synthesis, however recent advances in biotechnology have enabled industrial production using yeast and bacteria (Humbelin et al. (1999) J Indust Micro and Biotech 22:1-7). The biologically synthesized riboflavin is cheaper to produce, and the process is better for the environment.
Several enzymatic steps are required to take GTP to riboflavin. The first step in bacteria is catalyzed by a GTP cyclohydrolase II activity which takes GTP to 2,5-iamino-6-ribosylamino-4(3H)-pyrimidinone 5xe2x80x2-phosphate. The enzyme performing this step is encoded by the ribA gene. RibA has two enzymatic activities, the above mentioned cyclohydrolase and a 3,4-dihydroxy-2-butanone 4-phosphate synthase activity that takes ribulose 5-phosphate to L-3,4-dihydroxy-2-butanone-4-phosphate, which is combined to a pathway intermediate, to form 6,7-dimethyl-8-ribityllumazine, the penultimate intermediate to riboflavin. The second step in the pathway is encoded by ribG a riboflavin-specific deaminase.
Studies using riboflavin over-producing Bacillus subtilis strains, have led to the conclusion that the GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase enzyme is rate-limiting for high-level riboflavin accumulation (Humbelin et al. (1999) J Indust Micro and Biotech 22:1-7). Increasing the copy number of the ribA gene in these strains results in improved riboflavin productivity. The pathways leading to riboflavin biosynthesis are largely conserved between plants and bacteria. Therefore, the potential exists for improving the riboflavin content in crop plants, thus reducing the need for vitamin supplementation in food.
The present invention describes the identification and utility of GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase sequences from corn, rice, soybean, and wheat. Also disclosed are sequences from corn, rice, and wheat that encode riboflavin-specific deaminases. It is believed that modulation of these activities through over-expression, under-expression, or mutation will lead to altered levels of riboflavin in plants.
Hormones in animal systems and phytohormones in plants control many metabolic processes. Phytohormones differ in their structure and specific actions compared to animal hormones, though the signal transduction mechanisms involved may be similar in plants and animals. Phytohormones affect shoot elongation, stem elongation, root growth, seed dormancy, fruit ripening, leaf senescence and morphogenesis, disease resistance (Hoffman et al. (1999) Plant Physiol 119:935-949), to name a few.
Among the phytohormones that have been studied so far, ethylene is the simplest in terms of chemical structure. Its effects, however, are far-ranging, affecting seed dormancy, fruit ripening and abscission, flower development, leaf senescence, adventitious root formation, and shoot and root growth and differentiation. Ethylene is synthesized from methionine via three enzymatic steps. Methionine is converted to S-adenosyl-methionine (SAM) by SAM synthetase, which is then converted to 1-aminocyclopropane-1-carboxylic acid (ACC) by ACC synthase. Finally, ACC oxidase acts on ACC to yield ethylene. The genes encoding these enzymes have been cloned, and transgenic approaches based on these genes have been attempted to control ethylene levels, and consequently fruit ripening. Using antisense technology, ACC synthase or ACC oxidase activities have been reduced in transgenic plants leading to inhibition of fruit ripening (Hamilton et al. (1990) Nature 346:284-287; Oeller et al. (1991) Science 254:437-439).
The mechanisms by which ethylene regulates plant development however are yet to be clearly defined. Ethylene-insensitive mutants and constitutive ethylene response mutants, principally in Arabidopsis, have been valuable in outlining the ethylene response pathway (Kieber (1997) Annu. Rev. Plant Physiol. Plant Mol. Biol. 48:277-296). The isolation of the genes affected in these mutants indicates the involvement of a protein kinase cascade in ethylene signaling. CTR1, a negative regulator of the ethylene response encodes a serine/threonine kinase that is most similar to the Raf family of protein kinases (Kieber et al. (1993) Cell 72:427-441). ETR1 in which dominant mutations lead to defective ethylene responses encodes a protein that is similar to bacterial two-component histidine kinases (Chang et al. (1993) Science 262:539-544). It most probably serves as an ethylene receptor/ethylene response factor since etr1 mutant seedlings bind ethylene at reduced levels compared to wild-type (Bleecker et al. (1988) Science 241:1086-1089), the ETR1 protein has been shown to bind ethylene (Schaller and Bleeker (1995) Science 270:1809-1811), and genetic epistasis analysis puts ETR1 the start of the ethylene response pathway (Kieber et al. (1993)Cell 72:427-441). U.S. Pat. Nos. 5,689,055 and 5,824,868 describe the Arabidopsis ETR1 gene, its tomato homologs, and their use in generating transgenic plants with modified response to ethylene.
ETR1 belongs to a small gene family in Arabidopsis, and at least one ETR1 homolog in Arabidopsis, ERS, has already been cloned (Hua et al. (1995) Science 269:1712-1714). Homologs in other species like rice and tomato have been isolated as well (Wilkinson et al. (1995) Science 270:1807-1809; Yau and Yip (1997) Plant Physiol 115:315; Tieman and Klee (1999) Plant Physiol 120:165-172). Many questions however remain regarding ethylene response factor gene organization, evolution, structure and function. Accordingly, additional nucleic acid sequences encoding ethylene response factors are disclosed herein which would facilitate studies to better understand ethylene response factors and ethylene signaling in plants and could provide genetic tools to enhance or otherwise alter developmental and physiological processes regulated by ethylene.
Acyl-CoA thioesterases catalyze the hydrolysis of variable length acyl-CoAs to produce free fatty acids and CoASH. Acyl-CoA thioesterase activities are generally found in most organisms from prokaryotes to eukaryotes. Eukaryotic acyl-CoA thioesterase activities have been detected in various subcellular organelles including lysosomes, peroxisomes, and mitochondria, as well as in the cytosol. Long chain acyl-CoA esters are important intermediates in degradation and synthesis of fatty acids, and may have important roles in regulating intermediary metabolism and gene expression (Waku (1992) Biochem Biophys Acta 1124:101-111). In animal systems, free fatty acids and acyl-CoAs have been shown to be nuclear receptor ligands which regulate lipid homeostasis. Also, acyl-CoAs act as potent feedback inhibitors of fatty acid synthesis. Typically, fatty acids entering cells are rapidly esterified to their corresponding CoA-esters. These acyl-CoAs are then oxidized in mitochondria or peroxisomes, elongated, desaturated or esterified into complex lipids or transferred post-translationally to proteins. The precise role of acyl-CoA thioesterases, their substrates, and products is not yet fully understood. However it is clear that animal and yeast acyl-CoA thioesterase enzymes are involved in the regulation of lipid metabolism by modulation of cellular concentrations of acyl-CoAs and fatty acids. It is unclear at this time what role the acyl-CoA thioesterases play in plants although these enzymatic activities are well known in plants (Murphy et al. (1984) Eur J Biochem 142:43-48).
Previously, acyl-CoA thioesterases were thought to coordinate with the fatty acid synthases in the biosynthesis of fatty acids in the cytosol. Although this is true, recent findings of peroxisomal and mitochondrial forms of the enzyme implicate additional roles for the thioesterases since peroxisomes and mitochondria do not contain synthase activities (Hunt et al. (1999) J Biol Chem 274:34317-34326, Jones et al. (1999) J Biol Chem 274:9216-9223, and Liu et al. (1997) J Biol Chem 272:13779-13785). Many aspects of fatty acid utilization and regulation are tied into growth rates and the ability of plants to adapt to their environment. It is therefore likely that the acyl-CoA thioesterases will play some role in regulating plant metabolism, just as they do in animal systems.
Members of the superfamily of adenosine triphosphate (ATP)-binding-cassette (ABC) transport systems couple the hydrolysis of ATP to the translocation of solutes across a biological membrane. Recognized by their common modular organization and two sequence motifs that constitute a nucleotide binding fold, ABC transporters are widespread among all living organisms. They accomplish not only the uptake of nutrients in bacteria but are involved in diverse processes, such as signal transduction, protein secretion, drug and antibiotic resistance, antigen presentation, bacterial pathogenesis and sporulation. Moreover, some human inheritable diseases, like cystic fibrosis, adrenoleukodystrophy and Stargardt""s disease are caused by defective ABC transport systems. Details of the molecular mechanism by which these systems exert their functions are still poorly understood (Schneider, E. and Hunke, S. (1998) FEMS Microbiol Rev 22:1-20).
The pleiotropic drug resistance gene PDR5 encodes a protein which is a member of the ABC-transport protein superfamily. This ABC transporter functions as a drug extrusion pump by being involved in the ATP-dependent efflux of a variety of structurally unrelated cytotoxic compounds. The transcription regulators PDR1, PDR3, PDR7, and PDR9 control the expression of the gene PDR5 (Balzi, E. and Goffeau, A. (1995) J Bioenerg Biomembr 27:71-76). PDR5 encodes a 160-kDa protein with a predicted duplicated six membrane-spanning domain and a repeated putative ATP-binding domain. PDR5 shares this structural feature with the mammalian multidrug resistance pumps as well as the functional capacity of conferring resistance to various inhibitors upon amplification (Leppert, G. et al. (1990) Genetics 125:13-20). PDR5 homologs are present in plants, may function during stress conditions in an analogous fashion to that described in yeast, and expression of such ABC transporters is subject to a complex hormonal and environmental regulation (Smart, C. C. and Fleming, A. J. (1996) J Biol Chem 271:19351-19357).
Also a member of the ABC-superfamily, GCN20 uptakes ions and amino acids. GCN20 is co-immunoprecipitated from cell extracts with GCN 1, another factor required to activate GCN2, and the two proteins interact in the yeast two-hybrid system. These two factors indicate that GCN1 and GCN20 are components of a protein complex that couples the kinase activity of GCN2 to the availability of amino acids. GCN20 is closely related to ABC proteins identified in Caenorhabditis elegans, rice and humans, suggesting that the function of GCN20 may be conserved among diverse eukaryotic organisms (Vazquez de Aldana, C. R. et al. (1995) EMBO J 14:3184-3199). As part of the GCN1/GCN20 complex, GCN20 may be involved in the modulation of the EF3-related function which facilitates the activation of GCN2 by uncharged tRNA on translating ribosomes (Marton, M. J. et al. (1997) Mol Cell Biol 17:4474-4489).
ABC transporters play a role in the protection of organisms against exogenous toxins by cellular detoxification processes. P-glycoprotein, the product of the multidrug resistance (MDR1) gene, is an ATP-driven transmembrane pump that increases the resistance of cells by actively exporting toxic chemicals. In addition to transporting anticancer drugs, P-glycoprotein also extrudes steroid hormones and a variety of lipophilic drugs, such as calcium channel blockers, phenothiazines, cyclosporines, etc.
The 70-kDa peroxisomal membrane protein (PMP70) is one of the major integral membrane proteins of rat liver peroxisomes. The carboxyl-terminal region of PMP70 has strong sequence similarities to a group of ATP-binding proteins such as MalK and MDR. These proteins form a superfamily and are involved in various biological processes including membrane transport. The PMP70 protein is a transmembrane protein possibly forming a channel, with its ATP-binding domain exposed to the cytosol. PMP70 is involved in active transport across the peroxisomal membrane. (Kamijo, K. et al. (1990) J. Biol. Chem. 265:4534-4540).
Immunoblot analysis shows that PMP70 is associated with the peroxisomal membrane in liver, renal cortex, and jejunal mucosa (Usuda, N. et al. (1991) Cytochem 39:1357-1366). cDNAs for human and rat PMP70 have been cloned and sequenced and the gene mapped to human chromosome 1p21-22. In humans, mutations in the PMP70 gene have been found in a subset of patients with Zellweger-syndrome, a lethal inborn error of peroxisome biogenesis (Gartner, J. and Valle, D. (1993) i Semin Cell Biol 4:45-52). Members of an MDR-like gene family, with no similarity to PMP70, have been identified from an Arabidopsis thaliana cDNA library (Dudler, R. and Hertig, C. (1991) J. Biol. Chem. 267:5882-5888). No other plant MDR-like genes have been identified to date, although identification of these genes in plants will be useful to understand the herbicide resistance.
Plants produce cytotoxic compounds to which they are susceptible, and are exposed to exogenous toxins (microbial products, allelochemicals, and agrochemicals) making cell survival contingent on mechanisms for detoxifying these agents. One detoxification mechanism is the glutathione S-transferase-catalyzed glutathionation of the toxin, or an activated derivative, and transport of the conjugate out of the cytosol. The glutathione S-conjugate (GS-X) pump family is a new class of ATP-binding cassette (ABC) transporters responsible for the elimination and/or sequestration of pharmacologically and agronomically important compounds in mammalian, yeast and plant cells. The molecular structure and function of GS-X pumps encoded by mammalian and plant MRP, cMOAT (canalicular multispecific anion transporter), and YCF1 (yeast cadmium factor) genes have been conserved throughout molecular evolution. The physiologic function of GS-X pumps is closely related to cellular detoxification, oxidative stress, inflammation, and cancer drug resistance. Coordinated expression of GS-X pump genes, such as MRP1 and YCF1, and gamma-glutamylcystaine synthetase, a rate-limiting enzyme of cellular glutathione biosynthesis, is frequently observed (Ishikawa T. et al. (1997) Biosci. Rep. 17:189-207).
Four expressed sequence tags identified from an Arabidopsis cDNA library have deduced amino acid sequences which are highly similar to MRP and YCF1. These genes are differentially expressed in response to treatments of Arabidopsis with several herbicides, heavy metals and other toxic compounds indicating the involvement of different ABC transporters in different-detoxification mechanisms. The full-length cDNA from one of these ESTs (named AtMRP) has been sequenced and this information is present in GenBank (Accession No. U92650). At the amino acid level AtMRP is 34% identical to both MRP and YCF1 but its biochemical function has not been demonstrated (Tommasini, R. et al. (1997) FEBS Lett. 411:206-210).
An AtMRP1 gene which encodes a transporter responsible for the removal of glutathione S-conjugates from the cytosol has been isolated and sequenced. The AtMRP1 gene encodes an ABC transporter competent in the transport of glutathione S-conjugates of xenobiotics and endogenous substances, including herbicides and anthocyanins (Lu, Y. P. et al. (1997) Proc Natl Acad Sci USA 94:8243-8248). AtMRP1 possesses the same overall domain organization as HmMRP1 and ScYCF1. These three ABC transporters catalyze Mg-ATP-energized, vanadate-inhibitable transport of GS conjugates. A cDNA encoding a putative ABC transporter from Arabidopsis, AtMRP1 (not necessarily the same one as above), was identified based on sequence similarities to mammalian MRP1 (Marin, E. et al. (1998) Biochim Biophys Acta 1369:7-13).
Another gene, AtMRP2, from Arabidopsis has been isolated which is 87% identical at the amino acid level to AtMRP1 described by Lu et al. (1997) Proc Natl Acad Sci USA 94:8243-8248. This gene belongs to the same subclass of ABC transporter genes as AtMRP1, and its heterologous expression in yeast also confers Mg-ATP-energized GS conjugate transport. Besides transporting glutathione conjugates, AtMRP2 transports at high capacity Bn-NCC-1, a malonyl ester of the predominant nonfluorescent chlorophyll catabolite from Brassica napus. AtMRP2 simultaneously transports Bn-NCC-1 and GS conjugates without either substrate interfering with the transport of the other suggesting that the same pump may have both functions (Lu, Y. P. (1998) Plant Cell 10:267-282).
AtMRP3, another ABC-transporter from Arabidopsis thaliana exhibits high sequence similarity to the human (MRP1) and yeast (YCF1) glutathione-conjugate transporters and complements a cadmium-sensitive yeast mutant that also lacks glutathione-conjugate transport activity. The kinetic properties of AtMRP3 are very similar to those described for the vacuolar glutathione-conjugate transporter of barley and mung bean. AtMRP3 also is involved in the uptake of the chlorophyll catabolite Bn-NCC-1 (Tommasini, R. et al. (1998) Plant J. 13:773-780).
Also forming part of the Arabidopsis thaliana MRP gene family, encoding a putative GS-X pump, is AtMRP4. The derived amino acid sequence from AtMRP4 shares high levels of similarity (55-63%) with human, yeast, and other Arabidopsis homologues. Expression of the different members of the AtMRP gene family in Arabidopsis cell suspensions after treatment with chemicals that modify glutathione metabolism (compounds that induce different types of stress and that act as herbicide antidotes- safenus- in monocotyledonous species) reveals that the members of this gene family are differentially regulated (Sanchez-Fernandez, R. (1998) Mol. Gen. Genet: 258:655-662).
An isolated polynucleotide comprising a first nucleotide sequence selected from the group consisting of: (a) first nucleotide sequence encoding a polypeptide of at least 30 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202 and 204; or (b) a second nucleotide sequence comprising a complement of the first nucleotide sequence.
The present invention concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 351 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:2, 4, 6, and 8, 50, 82, 100 and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 72 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:12, 16, 18, 20, 22, 24, 26 and 28, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 110 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:10, 32, 36, 38, 40, 42, 44, 46, 48, 52, 60, 102, 104, 124 and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 189 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:14, 34, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 120, 122 and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 67 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:84, 86, 88, 90, 92, 94 and 96, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 87 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:98, 110, 112, 114, 116 and 118, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 155 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:128, 130, 132, 134, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 161 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:54, 136, 138, 140, 142 144, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 66 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166 168 and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 141 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:58, 106, 170, 172, 174, 176, 178, 180, 182 and 184 or (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 81 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:186, 188, 190, 192, 194, 196, 198, 200, 202, 204 and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of (a) a first nucleotide sequence encoding a polypeptide of at least 48 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:30, 56, 108, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
In a second embodiment, it is preferred that the isolated polynucleotide of the claimed invention comprises a nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:1, 3, 5, 7, 49, 81 and 99 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:2, 4, 6, 8, 50, 82 and 100.
Also in a second embodiment, it is preferred that the isolated polynucleotide of the claimed invention comprises a first nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:11, 15, 17, 19, 21, 23, 25 and 27 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:12, 16, 18, 20, 22, 24, 26 and 28.
Also in a second embodiment, it is preferred that the isolated polynucleotide of the claimed invention comprises a nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:9, 31, 35, 37, 39, 41, 43, 45, 47, 51, 59, 101, 103 and 123 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:10, 32, 36, 38, 40, 42, 44, 46, 48, 52, 60, 102, 104, and 124.
Also in a second embodiment, it is preferred that the isolated polynucleotide of the claimed invention comprises a nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:13, 33, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 119 and 121 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:14, 34, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 120 and 122.
Also in a second embodiment, it is preferred that the isolated polynucleotide of the claimed invention comprises a nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:83, 85, 87, 89, 91, 93 and 95 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:84, 86, 88, 90, 92, 94 and 96.
Also in a second embodiment, it is preferred that the isolated polynucleotide of the claimed invention comprises a nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:97, 109, 111, 113, 115 and 117 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:98, 110, 112, 114, 116 and 118.
Also in a second embodiment, it is preferred that the isolated polynucleotide of the claimed invention comprises a nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:127, 129, 131 and 133 that codes for the polypeptide selected from the group consisting of SEQ ID NOs: 128, 130, 132 and 134.
Also in a second embodiment, it is preferred that the isolated polynucleotide of the claimed invention comprises a nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:53, 135, 137, 139, 141 and 143 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:54, 136, 138, 140, 142 and 144.
Also in a second embodiment, it is preferred that the isolated polynucleotide of the claimed invention comprises a nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165 and 167 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166 and 168.
Also in a second embodiment, it is preferred that the isolated polynucleotide of the claimed invention comprises a nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:57, 105, 169, 171, 173, 175, 177, 179, 181 and 183 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:58, 106, 170, 172, 174, 176, 178, 180, 182 and 184.
Also in a second embodiment, it is preferred that the isolated polynucleotide of the claimed invention comprises a nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:185, 187, 189, 191, 193, 195, 197, 199, 201 and 203 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:186, 188, 190, 192, 194, 196, 198, 200, 202 and 204.
Also in a second embodiment, it is preferred that the isolated polynucleotide of the invention comprises a first nucleotide sequence which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:29, 55 and 107, that codes for the polypeptide selected from the group consisting of SEQ ID NOs:30, 56 and 108.
In a third embodiment, this invention concerns an isolated polynucleotide comprising a nucleotide sequence of at least one of 60 (preferably at least one of 40, most preferably at least one of 30) contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183 185, 187, 189, 191, 193, 195, 197, 199, 201 and 203 and the complement of such nucleotide sequences.
In a fourth embodiment, this invention relates to a chimeric gene comprising an isolated polynucleotide of the present invention operably linked to at least one suitable regulatory sequence.
In a fifth embodiment, the present invention concerns a host cell comprising a chimeric gene of the present invention or an isolated polynucleotide of the present invention. The host cell may be eukaryotic, such as a yeast or a plant cell, or prokaryotic, such as a bacterial cell. The present invention also relates to a virus, preferably a baculovirus, comprising an isolated polynucleotide of the present invention or a chimeric gene of the present invention.
In a sixth embodiment, the invention also relates to a process for producing a host cell comprising a chimeric gene of the present invention or an isolated polynucleotide of the present invention, the process comprising either transforming or transfecting a compatible host cell with a chimeric gene or isolated polynucleotide of the present invention.
In a seventh embodiment, the invention concerns a polypeptide of at least 351 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs:2, 4, 6, 8, 50, 82, and 100.
Also in a seventh embodiment, the invention concerns a polypeptide of at least 72 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs:12, 16, 18, 20, 22, 24, 26 and 28.
Also in a seventh embodiment, the invention concerns a polypeptide of at least 110 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs:10, 32, 36, 38, 40, 42, 44, 46, 48, 52, 60, 102, 104 and 124.
Also in a seventh embodiment, the invention concerns a polypeptide of at least 189 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs:14, 34, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 120 and 122.
Also in a seventh embodiment, the invention concerns a polypeptide of at least 67 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs:84, 86, 88, 90, 92, 94 and 96.
Also in a seventh embodiment, the invention concerns a polypeptide of at least 87 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs:98, 110, 112, 114, 116 and 118.
Also in a seventh embodiment, the invention concerns a polypeptide of at least 155 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs: 128, 130, 132 and 134.
Also in a seventh embodiment, the invention concerns a polypeptide of at least 161 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs:54, 136, 138, 140, 142 and 144.
Also in a seventh embodiment, the invention concerns a polypeptide of at least 66 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs:146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166 and 168.
Also in a seventh embodiment, the invention concerns a polypeptide of at least 141 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs:58, 106, 170, 172, 174, 176, 178, 180, 182 and 184.
Also in a seventh embodiment, the invention concerns a polypeptide of at least 81 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs:186, 188, 190, 192, 194, 196, 198, 200, 202 and 204.
Also in a seventh embodiment, the invention concerns a polypeptide of at least 48 amino acids comprising at least 80% identity based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs:30, 56 and 108.
In an eighth embodiment, the invention relates to a method of selecting an isolated polynucleotide that affects the level of expression of a dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polypeptide or enzyme activity in a host cell, preferably a plant cell, the method comprising the steps of: (a) constructing an isolated polynucleotide of the present invention or a chimeric gene of the present invention; (b) introducing the isolated polynucleotide or the chimeric gene into a host cell; (c) measuring the level of the dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polypeptide or enzyme activity in the host cell containing the isolated polynucleotide; and (d) comparing the level of the dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polypeptide or enzyme activity in the host cell containing the isolated polynucleotide with the level of the dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polypeptide or enzyme activity in the host cell that does not contain the isolated polynucleotide.
In a ninth embodiment, the invention concerns a method of obtaining a nucleic acid fragment encoding a substantial portion of a dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polypeptide, preferably a plant dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polypeptide, comprising the steps of: synthesizing an oligonucleotide primer comprising a nucleotide sequence of at least one of 60 (preferably at least one of 40, most preferably at least one of 30) contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID: NOs: dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter, and the complement of such nucleotide sequences; and amplifying a nucleic acid fragment (preferably a cDNA inserted in a cloning vector) using the oligonucleotide primer. The amplified nucleic acid fragment preferably will encode a substantial portion of a dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter amino acid sequence.
In a tenth embodiment, this invention relates to a method of obtaining a nucleic acid fragment encoding all or a substantial portion of the amino acid sequence encoding a dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polypeptide comprising the steps of: probing a cDNA or genomic library with an isolated polynucleotide of the present invention; identifying a DNA clone that hybridizes with an isolated polynucleotide of the present invention; isolating the identified DNA clone; and sequencing the cDNA or genomic fragment that comprises the isolated DNA clone.
In an eleventh embodiment, this invention concerns a composition, such as a hybridization mixture, comprising an isolated polynucleotide or polypeptide of the present invention.
In a twelfth embodiment, this invention concerns a method for positive selection of a transformed cell comprising: (a) transforming a host cell with the chimeric gene of the present invention or a construct of the present invention; and (b) growing the transformed host cell, preferably a plant cell, such as a monocot or a dicot, under conditions which allow expression of the dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polynucleotide in an amount sufficient to complement a null mutant to provide a positive selection means.
In a thirteenth embodiment, this invention relates to a method of altering the level of expression of a metabolism protein in a host cell comprising: (a) transforming a host cell with a chimeric gene of the present invention; and (b) growing the transformed host cell under conditions that are suitable for expression of the chimeric gene wherein expression of the chimeric gene results in production of altered levels of the metabolism proteins in the transformed host cell.
The invention can be more fully understood from the following detailed description and the accompanying Sequence Listing which form a part of this application.
Table 1 lists the polypeptides that are described herein, the designation of the cDNA clones that comprise the nucleic acid fragments encoding polypeptides representing all or a substantial portion of these polypeptides, and the corresponding identifier (SEQ ID NO:) as used in the attached Sequence Listing. The sequence descriptions and Sequence Listing attached hereto comply with the rules governing nucleotide and/or amino acid sequence disclosures in patent applications as set forth in 37 C.F.R. xc2xa71.821-1.825. Table 1 also identifies the cDNA clones as individual ESTs (xe2x80x9cESTxe2x80x9d), the sequences of the entire cDNA inserts comprising the indicated cDNA clones (xe2x80x9cFISxe2x80x9d), contigs assembled from two or more ESTs (xe2x80x9cContigxe2x80x9d), contigs assembled from an FIS and one or more ESTs (xe2x80x9cContig*xe2x80x9d), or sequences encoding the entire protein derived from an FIS, a contig, or an FIS and PCR (xe2x80x9cCGSxe2x80x9d).
Nucleotide sequences, SEQ ID NOs:1, 3, 5 and 7 and amino acid sequences SEQ ID NOs:2, 4, 6 and 8 were determined by further sequence analysis of cDNA clones encoding the amino acid sequences set forth in SEQ ID NOs:10, 12, 14 and 16. Nucleotide SEQ ID NOs:9, 11, 13 and 15 amino acid SEQ ID NOs:10, 12, 14 and 16 were presented in a U.S. Provisional Application No. 60/143,401, filed Jul. 12, 1999.
Nucleotide sequences, SEQ ID NOs:17, 21 and 23 and amino acid sequences SEQ ID NOs:18, 20 and 24 were determined by further sequence analysis of cDNA clones encoding the amino acid sequences set forth in SEQ ID NOs:30, 32 and 34. Nucleotide SEQ ID NOs:25, 27, 29, 31 and 33 amino acid SEQ ID NOs:26, 28, 30, 32 and 34 were presented in a U.S. Provisional Application No. 60/143,412, filed Jul. 12, 1999.
Nucleotide sequences, SEQ ID NOs:35, 37, 39, 41, 43 and 45 and amino acid sequences SEQ ID NOs:36, 38, 40, 42, 44 and 46 were determined by further sequence analysis of cDNA clones encoding the amino acid sequences set forth in SEQ ID NOs:50, 52, 54, 56, 58 and 60. Nucleotide SEQ ID NOs:47, 49, 51. 53. 55, 57 and 59 amino acid SEQ ID NOs:48, 50, 52, 54, 56, 58 and 60 were presented in a U.S. Provisional Application No. 60/146,650 filed Jul. 30, 1999.
Nucleotide sequence, SEQ ID NO:69 and amino acid sequence SEQ ID NO:70, were determined by further sequence analysis of cDNA clones encoding the amino acid sequence set forth in SEQ ID NO:82. Nucleotide SEQ ID NOs:65, 73 and 81 amino acid SEQ ID NOs:66, 74 and 82 were presented in a U.S. Provisional Application No. 60/170,906 filed Dec. 14, 1999.
Nucleotide sequences, SEQ ID NOs:85, 87, 89, 91, 93 and 95 and amino acid sequences SEQ ID NOs:84, 86, 88, 90, 92, 94 and 96, were determined by further sequence analysis of cDNA clones encoding the amino acid sequences set forth in SEQ ID NOs:100, 102, 104, 106, 108 and 110. Nucleotide SEQ ID NOs:97, 99, 101, 103, 105, 107 and 109 and amino acid SEQ ID NOs:98, 100, 102, 104, 106, 108 and 110 were presented in a U.S. Provisional Application No. 60/172,959 filed Dec. 21, 1999.
Nucleotide sequences, SEQ ID NOs:109, 111, 115 and 117 and amino acid sequences SEQ ID NOs:110, 112, 116 and 118, were determined by further sequence analysis of cDNA clones encoding the amino acid sequences set forth in SEQ ID NO:120, 122, 124 and 126. Nucleotide SEQ ID NOs:113, 119, 121, 123 and 125 amino acid SEQ ID NOs:114, 120, 122, 124 and 126 were presented in a U.S. Provisional Application No. 60/172,946 filed Dec. 21, 1999.
The Sequence Listing contains the one letter code for nucleotide sequence characters and the three letter codes for amino acids as defined in conformity with the IUPAC-IUBMB standards described in Nucleic Acids Res. 13:3021-3030 (1985) and in the Biochemical J. 219 (No. 2):345-373 (1984) which are herein incorporated by reference. The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. xc2xa71.822.
In the context of this disclosure, a number of terms shall be utilized. The terms xe2x80x9cpolynucleotidexe2x80x9d, xe2x80x9cpolynucleotide sequencexe2x80x9d, xe2x80x9cnucleic acid sequencexe2x80x9d, and xe2x80x9cnucleic acid fragmentxe2x80x9d/xe2x80x9cisolated nucleic acid fragmentxe2x80x9d are used interchangeably herein. These terms encompass nucleotide sequences and the like. A polynucleotide may be a polymer of RNA or DNA that is single- or double-stranded, that optionally contains synthetic, non-natural or altered nucleotide bases. A polynucleotide in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA, synthetic DNA, or mixtures thereof. An isolated polynucleotide of the present invention may include at least one of 60 contiguous nucleotides, preferably at least one of 40 contiguous nucleotides, most preferably one of at least 30 contiguous nucleotides derived from SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183 185, 187, 189, 191, 193, 195, 197, 199, 201 and 203, or the complement of such sequences.
The term xe2x80x9cisolated polynucleotidexe2x80x9d refers to a polynucleotide that is substantially free from other nucleic acid sequences, such as and not limited to other chromosomal and extrachromosomal DNA and RNA, that normally accompany or interact with it as found in its naturally occuring environment. Isolated polynucleotides may be purified from a host cell in which they naturally occur. Conventional nucleic acid purification methods known to skilled artisans may be used to obtain isolated polynucleotides. The term also embraces recombinant polynucleotides and chemically synthesized polynucleotides.
The term xe2x80x9crecombinantxe2x80x9d means, for example, that a nucleic acid sequence is made by an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis or by the manipulation of isolated nucleic acids by genetic engineering techniques.
As used herein, xe2x80x9ccontigxe2x80x9d refers to a nucleotide sequence that is assembled from two or more constituent nucleotide sequences that share common or overlapping regions of sequence homology. For example, the nucleotide sequences of two or more nucleic acid fragments can be compared and aligned in order to identify common or overlapping sequences. Where common or overlapping sequences exist between two or more nucleic acid fragments, the sequences (and thus their corresponding nucleic acid fragments) can be assembled into a single contiguous nucleotide sequence.
As used herein, xe2x80x9csubstantially similarxe2x80x9d refers to nucleic acid fragments wherein changes in one or more nucleotide bases results in substitution of one or more amino acids, but do not affect the functional properties of the polypeptide encoded by the nucleotide sequence. xe2x80x9cSubstantially similarxe2x80x9d also refers to nucleic acid fragments wherein changes in one or more nucleotide bases does not affect the ability of the nucleic acid fragment to mediate alteration of gene expression by gene silencing through for example antisense or co-suppression technology. xe2x80x9cSubstantially similarxe2x80x9d also refers to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotides that do not substantially affect the functional properties of the resulting transcript vis-a-vis the ability to mediate gene silencing or alteration of the functional properties of the resulting protein molecule. It is therefore understood that the invention encompasses more than the specific exemplary nucleotide or amino acid sequences and includes functional equivalents thereof. The terms xe2x80x9csubstantially similarxe2x80x9d and xe2x80x9ccorresponding substantiallyxe2x80x9d are used interchangeably herein.
Substantially similar nucleic acid fragments may be selected by screening nucleic acid fragments representing subfragments or modifications of the nucleic acid fragments of the instant invention, wherein one or more nucleotides are substituted, deleted and/or inserted, for their ability to affect the level of the polypeptide encoded by the unmodified nucleic acid fragment in a plant or plant cell. For example, a substantially similar nucleic acid fragment representing at least one of 30 contiguous nucleotides derived from the instant nucleic acid fragment can be constructed and introduced into a plant or plant cell. The level of the polypeptide encoded by the unmodified nucleic acid fragment present in a plant or plant cell exposed to the substantially similar nucleic fragment can then be compared to the level of the polypeptide in a plant or plant cell that is not exposed to the substantially similar nucleic acid fragment.
For example, it is well known in the art that antisense suppression and co-suppression of gene expression may be accomplished using nucleic acid fragments representing less than the entire coding region of a gene, and by using nucleic acid fragments that do not share 100% sequence identity with the gene to be suppressed. Moreover, alterations in a nucleic acid fragment which result in the production of a chemically equivalent amino acid at a given site, but do not effect the functional properties of the encoded polypeptide, are well known in the art. Thus, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue, such as glycine, or a more hydrophobic residue, such as valine, leucine, or isoleucine. Similarly, changes which result in substitution of one negatively charged residue for another, such as aspartic acid for glutamic acid, or one positively charged residue for another, such as lysine for arginine, can also be expected to produce a functionally equivalent product. Nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the polypeptide molecule would also not be expected to alter the activity of the polypeptide. Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products. Consequently, an isolated polynucleotide comprising a nucleotide sequence of at least one of 60 (preferably at least one of 40, most preferably at least one of 30) contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183 185, 187, 189, 191, 193, 195, 197, 199, 201 and 203, and the complement of such nucleotide sequences may be used in methods of selecting an isolated polynucleotide that affects the expression of a dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polypeptide in a host cell. A method of selecting an isolated polynucleotide that affects the level of expression of a polypeptide in a virus or in a host cell (eukaryotic, such as plant or yeast, prokaryotic such as bacterial) may comprise the steps of: constructing an isolated polynucleotide of the present invention or a chimeric gene of the present invention; introducing the isolated polynucleotide or the chimeric gene into a host cell; measuring the level of a polypeptide or enzyme activity in the host cell containing the isolated polynucleotide; and comparing the level of a polypeptide or enzyme activity in the host cell containing the isolated polynucleotide with the level of a polypeptide or enzyme activity in a host cell that does not contain the isolated polynucleotide.
Moreover, substantially similar nucleic acid fragments may also be characterized by their ability to hybridize. Estimates of such homology are provided by either DNA-DNA or DNA-RNA hybridization under conditions of stringency as is well understood by those skilled in the art (Hames and Higgins, Eds. (1985) Nucleic Acid Hybridisation, IRL Press, Oxford, U.K.). Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms. Post-hybridization washes determine stringency conditions. One set of preferred conditions uses a series of washes starting with 6xc3x97SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2xc3x97SSC, 0.5% SDS at 45xc2x0 C. for 30 min, and then repeated twice with 0.2xc3x97SSC, 0.5% SDS at 50xc2x0 C. for 30 min. A more preferred set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2xc3x97SSC, 0.5% SDS which was increased to 60xc2x0 C. Another preferred set of highly stringent conditions uses two final washes in 0.1xc3x97SSC, 0.1% SDS at 65xc2x0 C.
Substantially similar nucleic acid fragments of the instant invention may also be characterized by the percent identity of the amino acid sequences that they encode to the amino acid sequences disclosed herein, as determined by algorithms commonly employed by those skilled in this art. Suitable nucleic acid fragments (isolated polynucleotides of the present invention) encode polypeptides that are at least about 70% identical, preferably at least about 80% identical to the amino acid sequences reported herein. Preferred nucleic acid fragments encode amino acid sequences that are about 85% identical to the amino acid sequences reported herein. More preferred nucleic acid fragments encode amino acid sequences that are at least about 90% identical to the amino acid sequences reported herein. Most preferred are nucleic acid fragments that encode amino acid sequences that are at least about 95% identical to the amino acid sequences reported herein. Suitable nucleic acid fragments not only have the above identities but typically encode a polypeptide having at least 50 amino acids, preferably at least 100 amino acids, more preferably at least 150 amino acids, still more preferably at least 200 amino acids, and most preferably at least 250 amino acids. Sequence alignments and percent identity calculations were performed using the Megalign program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequences was performed using the Clustal method of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments using the Clustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5.
A xe2x80x9csubstantial portionxe2x80x9d of an amino acid or nucleotide sequence comprises an amino acid or a nucleotide sequence that is sufficient to afford putative identification of the protein or gene that the amino acid or nucleotide sequence comprises. Amino acid and nucleotide sequences can be evaluated either manually by one skilled in the art, or by using computer-based sequence comparison and identification tools that employ algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul et al. (1993) J. Mol. Biol. 215:403-410). In general, a sequence of ten or more contiguous amino acids or thirty or more contiguous nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene-specific oligonucleotide probes comprising 30 or more contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12 or more nucleotide, may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a xe2x80x9csubstantial portionxe2x80x9d of a nucleotide sequence comprises a nucleotide sequence that will afford specific identification and/or isolation of a nucleic acid fragment comprising the sequence. The instant specification teaches amino acid and nucleotide sequences encoding polypeptides that comprise one or more particular plant proteins. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above.
xe2x80x9cCodon degeneracyxe2x80x9d refers to divergence in the genetic code permitting variation of the nucleotide sequence without effecting the amino acid sequence of an encoded polypeptide. Accordingly, the instant invention relates to any nucleic acid fragment comprising a nucleotide sequence that encodes all or a substantial portion of the amino acid sequences set forth herein. The skilled artisan is well aware of the xe2x80x9ccodon-biasxe2x80x9d exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a nucleic acid fragment for improved expression in a host cell, it is desirable to design the nucleic acid fragment such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.
xe2x80x9cSynthetic nucleic acid fragmentsxe2x80x9d can be assembled from oligonucleotide building blocks that are chemically synthesized using procedures known to those skilled in the art. These building blocks are ligated and annealed to form larger nucleic acid fragments which may then be enzymatically assembled to construct the entire desired nucleic acid fragment. xe2x80x9cChemically synthesizedxe2x80x9d, as related to a nucleic acid fragment, means that the component nucleotides were assembled in vitro. Manual chemical synthesis of nucleic acid fragments may be accomplished using well established procedures, or automated chemical synthesis can be performed using one of a number of commercially available machines. Accordingly, the nucleic acid fragments can be tailored for optimal gene expression based on optimization of the nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene expression if codon usage is biased towards those codons favored by the host. Determination of preferred codons can be based on a survey of genes derived from the host cell where sequence information is available.
xe2x80x9cGenexe2x80x9d refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5xe2x80x2 non-coding sequences) and following (3xe2x80x2 non-coding sequences) the coding sequence. xe2x80x9cNative genexe2x80x9d refers to a gene as found in nature with its own regulatory sequences. xe2x80x9cChimeric genexe2x80x9d refers any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. xe2x80x9cEndogenous genexe2x80x9d refers to a native gene in its natural location in the genome of an organism. A xe2x80x9cforeign genexe2x80x9d refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A xe2x80x9ctransgenexe2x80x9d is a gene that has been introduced into the genome by a transformation procedure.
xe2x80x9cCoding sequencexe2x80x9d refers to a nucleotide sequence that codes for a specific amino acid sequence. xe2x80x9cRegulatory sequencesxe2x80x9d refers to nucleotide sequences located upstream (5xe2x80x2 non-coding sequences), within, or downstream (3xe2x80x2 non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, and polyadenylation recognition sequences.
xe2x80x9cPromoterxe2x80x9d refers to a nucleotide sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3xe2x80x2 to a promoter sequence. The promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an xe2x80x9cenhancerxe2x80x9d is a nucleotide sequence which can stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter. Promoters may be derived in their entirety from a native gene, or may be composed of different elements derived from different promoters found in nature, or may even comprise synthetic nucleotide segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. Promoters which cause a nucleic acid fragment to be expressed in most cell types at most times are commonly referred to as xe2x80x9cconstitutive promotersxe2x80x9d. New promoters of various types useful in plant cells are constantly being discovered; numerous examples may be found in the compilation by Okamuro and Goldberg (1989) Biochemistry of Plants 15:1-82. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, nucleic acid fragments of different lengths may have identical promoter activity.
xe2x80x9cTranslation leader sequencexe2x80x9d refers to a nucleotide sequence located between the promoter sequence of a gene and the coding sequence. The translation leader sequence is present in the fully processed mRNA upstream of the translation start sequence. The translation leader sequence may affect processing of the primary transcript to mRNA, mRNA stability or translation efficiency. Examples of translation leader sequences have been described (Turner and Foster (1995) Mol. Biotechnol. 3:225-236).
xe2x80x9c3xe2x80x2 Non-coding sequencesxe2x80x9d refers to nucleotide sequences located downstream of a coding sequence and includes polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3xe2x80x2 end of the mRNA precursor. The use of different 3 non-coding sequences is exemplified by Ingelbrecht et al. (1989)Plant Cell 1:671-680.
xe2x80x9cRNA transcriptxe2x80x9d refers to the product resulting from RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be a RNA sequence derived from posttranscriptional processing of the primary transcript and is referred to as the mature RNA. xe2x80x9cMessenger RNA (mRNA)xe2x80x9d refers to the RNA that is without introns and can be translated into polypeptides by the cell. xe2x80x9ccDNAxe2x80x9d refers to DNA that is complementary to and derived from an mRNA template. The cDNA can be single-stranded or converted to double stranded form using, for example, the Klenow fragment of DNA polymerase I. xe2x80x9cSense RNAxe2x80x9d refers to an RNA transcript that includes the mRNA and can be translated into a polypeptide by the cell. xe2x80x9cAntisense RNAxe2x80x9d refers to an RNA transcript that is complementary to all or part of a target primary transcript or mRNA and that blocks the expression of a target gene (see U.S. Pat. No. 5,107,065, incorporated herein by reference). The complementarity of an antisense RNA may be with any part of the specific nucleotide sequence, i.e., at the 5xe2x80x2 non-coding sequence, 3xe2x80x2 non-coding sequence, introns, or the coding sequence. xe2x80x9cFunctional RNAxe2x80x9d refers to sense RNA, antisense RNA, ribozyme RNA, or other RNA that may not be translated but yet has an effect on cellular processes.
The term xe2x80x9coperably linkedxe2x80x9d refers to the association of two or more nucleic acid fragments so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.
The term xe2x80x9cexpressionxe2x80x9d, as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment of the invention. xe2x80x9cExpressionxe2x80x9d may also refer to translation of mRNA into a polypeptide. xe2x80x9cAntisense inhibitionxe2x80x9d refers to the production of antisense RNA transcripts capable of suppressing the expression of the target protein. xe2x80x9cOverexpressionxe2x80x9d refers to the production of a gene product in transgenic organisms that exceeds levels of production in normal or non-transformed organisms. xe2x80x9cCo-suppressionxe2x80x9d refers to the production of sense RNA transcripts capable of suppressing the expression of identical or substantially similar foreign or endogenous genes (U.S. Pat. No. 5,231,020, incorporated herein by reference).
A xe2x80x9cproteinxe2x80x9d or xe2x80x9cpolypeptidexe2x80x9d is a chain of amino acids arranged in a specific order determined by the coding sequence in a polynucleotide encoding the polypeptide. Each protein or polypeptide has a unique function.
xe2x80x9cAltered levelsxe2x80x9d or xe2x80x9caltered expressionxe2x80x9d refers to the production of gene product(s) in transgenic organisms in amounts or proportions that differ from that of normal or non-transformed organisms.
xe2x80x9cNull mutantxe2x80x9d refers to a host cell which either lacks the expression of a certain polypeptide or expresses a polypeptide which is inactive or does not have any detectable expected enzymatic function.
xe2x80x9cMature proteinxe2x80x9d or the term xe2x80x9cmaturexe2x80x9d when used in describing a protein refers to a post-translationally processed polypeptide; i.e., one from which any pre- or propeptides present in the primary translation product have been removed. xe2x80x9cPrecursor proteinxe2x80x9d or the term xe2x80x9cprecursorxe2x80x9d when used in describing a protein refers to the primary product of translation of mRNA; i.e., with pre- and propeptides still present. Pre- and propeptides may be but are not limited to intracellular localization signals.
A xe2x80x9cchloroplast transit peptidexe2x80x9d is an amino acid sequence which is translated in conjunction with a protein and directs the protein to the chloroplast or other plastid types present in the cell in which the protein is made. xe2x80x9cChloroplast transit sequencexe2x80x9d refers to a nucleotide sequence that encodes a chloroplast transit peptide. A xe2x80x9csignal peptidexe2x80x9d is an amino acid sequence which is translated in conjunction with a protein and directs the protein to the secretory system (Chrispeels (1991) Ann. Rev. Plant Phys. Plant Mol. Biol. 42:21-53). If the protein is to be directed to a vacuole, a vacuolar targeting signal (supra) can further be added, or if to the endoplasmic reticulum, an endoplasmic reticulum retention signal (supra) may be added. If the protein is to be directed to the nucleus, any signal peptide present should be removed and instead a nuclear localization signal included (Raikhel (1992) Plant Phys. 100:1627-1632).
xe2x80x9cTransformationxe2x80x9d refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as xe2x80x9ctransgenicxe2x80x9d organisms. Examples of methods of plant transformation include Agrobacterium-mediated transformation (De Blaere et al. (1987) Meth. Enzymol. 143:277) and particle-accelerated or xe2x80x9cgene gunxe2x80x9d transformation technology (Klein et al. (1987) Nature (London) 327:70-73; U.S. Pat. No. 4,945,050, incorporated herein by reference). Thus, isolated polynucleotides of the present invention can be incorporated into recombinant constructs, typically DNA constructs, capable of introduction into and replication in a host cell. Such a construct can be a vector that includes a replication system and sequences that are capable of transcription and translation of a polypeptide-encoding sequence in a given host cell. A number of vectors suitable for stable transfection of plant cells or for the establishment of transgenic plants have been described in, e.g., Pouwels et al., Cloning Vectors: A Laboratory Manual, 1985, supp. 1987; Weissbach and Weissbach, Methods for Plant Molecular Biology, Academic Press, 1989; and Flevin et al., Plant Molecular Biology Manual, Kluwer Academic Publishers, 1990. Typically, plant expression vectors include, for example, one or more cloned plant genes under the transcriptional control of 5xe2x80x2 and 3xe2x80x2 regulatory sequences and a dominant selectable marker. Such plant expression vectors also can contain a promoter regulatory region (e.g., a regulatory region controlling inducible or constitutive, environmentally- or developmentally-regulated, or cell- or tissue-specific expression), a transcription initiation start site, a ribosome binding site, an RNA processing signal, a transcription termination site, and/or a polyadenylation signal.
Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described more fully in Sambrook et al. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989 (hereinafter xe2x80x9cManiatisxe2x80x9d).
xe2x80x9cPCRxe2x80x9d or xe2x80x9cpolymerase chain reactionxe2x80x9d is well known by those skilled in the art as a technique used for the amplification of specific DNA segments (U.S. Pat. Nos. 4,683,195 and 4,800,159).
The present invention concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) first nucleotide sequence encoding a polypeptide of at least 351 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:2, 4, 6, 8, 50, 82 and 100 and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) first nucleotide sequence encoding a polypeptide of at least 72 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:12, 16, 18, 20, 22, 24, 26 and 28, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) first nucleotide sequence encoding a polypeptide of at least 110 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:10, 32, 36, 38, 40, 42, 44, 46, 48, 52, 60, 102, 104, 124or (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 189 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:14, 34, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 120, 122 and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 67 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:84, 86, 88, 90, 92, 94 and 96, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 87 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:98, 110, 112, 114, 116 and 118, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 155 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:128, 130, 132, and 134 and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 161 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:54, 136, 138, 140, 142 and 144 and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 66 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs: 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166 and 168 and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 141 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:58, 106, 170, 172, 174, 176, 178, 180, 182 and 184, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 81 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:186, 188, 190, 192, 194, 196, 198, 200, 202 and 204, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
The present invention also concerns an isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence encoding a polypeptide of at least 48 amino acids having at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:30, 56 and 108, and (b) a second nucleotide sequence comprising the complement of the first nucleotide sequence.
Preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:1, 3, 5, 7, 49, 81 and 99 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:2, 4, 6, 8, 50, 82 and 100.
Also preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:11, 15, 17, 19, 21, 23, 25 and 27, that codes for the polypeptide selected from the group consisting of SEQ ID NOs:12, 16, 18, 20, 22, 24, 26 and 28.
Also preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:9, 31, 35, 37, 39, 41, 43, 45, 47, 51, 59, 101, 103 and 123 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:10, 32, 36, 38, 40, 42, 44, 46, 48, 52, 60, 102, 104 and 124.
Also preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:13, 33, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 119, 121 that codes for the polypeptide selected from the group consisting of SEQ ID NOs:14, 34, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 120 and 122.
Also preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:83, 85, 87, 89, 91, 93 and 95, that codes for the polypeptide selected from the group consisting of SEQ ID NOs:84, 86, 88, 90, 92, 94 and 96.
Also preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:97, 109, 111, 113, 115 and 117, that codes for the polypeptide selected from the group consisting of SEQ ID NOs:98, 110, 112, 114, 116 and 118.
Also preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:127, 129, 131 and 133, that codes for the polypeptide selected from the group consisting of SEQ ID NOs:128, 130, 132 and 134.
Also preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:53, 135, 137, 139, 141 and 143, that codes for the polypeptide selected from the group consisting of SEQ ID NOs:54, 136, 138, 140, 142 and 144.
Also preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165 and 167, that codes for the polypeptide selected from the group consisting of SEQ ID NOs:146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166 and 168.
Also preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:57, 105, 169, 171, 173, 175, 177, 179, 181 and 183, that codes for the polypeptide selected from the group consisting of SEQ ID NOs:58, 106, 170, 172, 174, 176, 178, 180, 182 and 184.
Also preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:185, 187, 189, 191, 193, 195, 197, 199, 201 and 203, that codes for the polypeptide selected from the group consisting of SEQ ID NOs:186, 188, 190, 192, 194, 196, 198, 200, 202 and 204.
Also preferably, the first nucleotide sequence comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:29, 55 and 107, that codes for the polypeptide selected from the group consisting of SEQ ID NOs:30, 56 and 108.
Nucleic acid fragments encoding at least a substantial portion of several metabolism proteins have been isolated and identified by comparison of random plant cDNA sequences to public databases containing nucleotide and protein sequences using the BLAST algorithms well known to those skilled in the art. The nucleic acid fragments of the instant invention may be used to isolate cDNAs and genes encoding homologous proteins from the same or other plant species. Isolation of homologous genes using sequence-dependent protocols is well known in the art. Examples of sequence-dependent protocols include, but are not limited to, methods of nucleic acid hybridization, and methods of DNA and RNA amplification as exemplified by various uses of nucleic acid amplification technologies (e.g., polymerase chain reaction, ligase chain reaction).
For example, genes encoding other dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter proteins, either as cDNAs or genomic DNAs, could be isolated directly by using all or a substantial portion of the instant nucleic acid fragments as DNA hybridization probes to screen libraries from any desired plant employing methodology well known to those skilled in the art. Specific oligonucleotide probes based upon the instant nucleic acid sequences can be designed and synthesized by methods known in the art (Maniatis). Moreover, an entire sequence(s) can be used directly to synthesize DNA probes by methods known to the skilled artisan such as random primer DNA labeling, nick translation, end-labeling techniques, or RNA probes using available in vitro transcription systems. In addition, specific primers can be designed and used to amplify a part or all of the instant sequences. The resulting amplification products can be labeled directly during amplification reactions or labeled after amplification reactions, and used as probes to isolate full length cDNA or genomic fragments under conditions of appropriate stringency.
In addition, two short segments of the instant nucleic acid fragments may be used in polymerase chain reaction protocols to amplify longer nucleic acid fragments encoding homologous genes from DNA or RNA. The polymerase chain reaction may also be performed on a library of cloned nucleic acid fragments wherein the sequence of one primer is derived from the instant nucleic acid fragments, and the sequence of the other primer takes advantage of the presence of the polyadenylic acid tracts to the 3xe2x80x2 end of the mRNA precursor encoding plant genes. Alternatively, the second primer sequence may be based upon sequences derived from the cloning vector. For example, the skilled artisan can follow the RACE protocol (Frohman et al. (1988) Proc. Natl. Acad. Sci. USA 85:8998-9002) to generate cDNAs by using PCR to amplify copies of the region between a single point in the transcript and the 3xe2x80x2 or 5xe2x80x2 end. Primers oriented in the 3xe2x80x2 and 5xe2x80x2 directions can be designed from the instant sequences. Using commercially available 3xe2x80x2 RACE or 5xe2x80x2 RACE systems (BRL), specific 3xe2x80x2 or 5xe2x80x2 cDNA fragments can be isolated (Ohara et al. (1989) Proc. Natl. Acad. Sci. USA 86:5673-5677; Loh et al. (1989) Science 243:217-220). Products generated by the 3xe2x80x2 and 5xe2x80x2 RACE procedures can be combined to generate full-length cDNAs (Frohman and Martin (1989) Techniques 1:165). Consequently, a polynucleotide comprising a nucleotide sequence of at least one of 60 (preferably one of at least 40, most preferably one of at least 30) contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183 185, 187, 189, 191, 193, 195, 197, 199, 201 and 203 and the complement of such nucleotide sequences may be used in such methods to obtain a nucleic acid fragment encoding a substantial portion of an amino acid sequence of a polypeptide.
The present invention relates to a method of obtaining a nucleic acid fragment encoding a substantial portion of a dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polypeptide, preferably a substantial portion of a plant dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polypeptide, comprising the steps of: synthesizing an oligonucleotide primer comprising a nucleotide sequence of at least one of 60 (preferably at least one of 40, most preferably at least one of 30) contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183 185, 187, 189, 191, 193, 195, 197, 199, 201 and 203, and the complement of such nucleotide sequences; and amplifying a nucleic acid fragment (preferably a cDNA inserted in a cloning vector) using the oligonucleotide primer. The amplified nucleic acid fragment preferably will encode a portion of a dioxygenase, Ent-kaurene synthase A, Ent-Kaurene synthase B, GA-20 or Gibberellin 3-beta Hydroxylase, GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate, riboflavin specific deaminase, ethylene response factor, acyl-CoA thioesterase, GCN20-like ABC transporter, PDR5-like ABC transporter, P-glycoprotein, ABC transporter or MRP4 ABC transporter polypeptide.
Availability of the instant nucleotide and deduced amino acid sequences facilitates immunological screening of cDNA expression libraries. Synthetic peptides representing substantial portions of the instant amino acid sequences may be synthesized. These peptides can be used to immunize animals to produce polyclonal or monoclonal antibodies with specificity for peptides or proteins comprising the amino acid sequences. These antibodies can be then be used to screen cDNA expression libraries to isolate full-length cDNA clones of interest (Lerner (1984) Adv. Immunol. 36:1-34; Maniatis).
In another embodiment, this invention concerns viruses and host cells comprising either the chimeric genes of the invention as described herein or an isolated polynucleotide of the invention as described herein. Examples of host cells which can be used to practice the invention include, but are not limited to, yeast, bacteria, and plants.
As was noted above, the nucleic acid fragments of the instant invention may be used to create transgenic plants in which the disclosed polypeptides are present at higher or lower levels than normal or in cell types or developmental stages in which they are not normally found. This would have the effect of altering the level of activity of those proteins and subsequently modifying specific metabolic steps in those cells.
Overexpression of the proteins of the instant invention may be accomplished by first constructing a chimeric gene in which the coding region is operably linked to a promoter capable of directing expression of a gene in the desired tissues at the desired stage of development. The chimeric gene may comprise promoter sequences and translation leader sequences derived from the same genes. 3xe2x80x2 Non-coding sequences encoding transcription termination signals may also be provided. The instant chimeric gene may also comprise one or more introns in order to facilitate gene expression.
Plasmid vectors comprising the instant isolated polynucleotide (or chimeric gene) may be constructed. The choice of plasmid vector is dependent upon the method that will be used to transform host plants. The skilled artisan is well aware of the genetic elements that must be present on the plasmid vector in order to successfully transform, select and propagate host cells containing the chimeric gene. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones et al. (1985) EMBO J. 4:2411-2418; De Almeida et al. (1989) Mol. Gen. Genetics 218:78-86), and thus that multiple events must be screened in order to obtain lines displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA, Northern analysis of mRNA expression, Western analysis of protein expression, or phenotypic analysis.
For some applications it may be useful to direct the instant polypeptides to different cellular compartments, or to facilitate their secretion from the cell. It is thus envisioned that the chimeric gene described above may be further supplemented by directing the coding sequence to encode the instant polypeptides with appropriate intracellular targeting sequences such as transit sequences (Keegstra (1989) Cell 56:247-253), signal sequences or sequences encoding endoplasmic reticulum localization (Chrispeels (1991) Ann. Rev. Plant Phys. Plant Mol. Biol. 42:21-53), or nuclear localization signals (Raikhel (1992) Plant Phys. 100:1627-1632) with or without removing targeting sequences that are already present. While the references cited give examples of each of these, the list is not exhaustive and more targeting signals of use may be discovered in the future.
It may also be desirable to reduce or eliminate expression of genes encoding the instant polypeptides in plants for some applications. In order to accomplish this, a chimeric gene designed for co-suppression of the instant polypeptide can be constructed by linking a gene or gene fragment encoding that polypeptide to plant promoter sequences. Alternatively, a chimeric gene designed to express anti sense RNA for all or part of the instant nucleic acid fragment can be constructed by linking the gene or gene fragment in reverse orientation to plant promoter sequences. Either the co-suppression or antisense chimeric genes could be introduced into plants via transformation wherein expression of the corresponding endogenous genes are reduced or eliminated.
Molecular genetic solutions to the generation of plants with altered gene expression have a decided advantage over more traditional plant breeding approaches. Changes in plant phenotypes can be produced by specifically inhibiting expression of one or more genes by antisense inhibition or cosuppression (U.S. Pat. Nos. 5,190,931, 5,107,065 and 5,283,323). An antisense or cosuppression construct would act as a dominant negative regulator of gene activity. While conventional mutations can yield negative regulation of gene activity these effects are most likely recessive. The dominant negative regulation available with a transgenic approach may be advantageous from a breeding perspective. In addition, the ability to restrict the expression of a specific phenotype to the reproductive tissues of the plant by the use of tissue specific promoters may confer agronomic advantages relative to conventional mutations which may have an effect in all tissues in which a mutant gene is ordinarily expressed.
The person skilled in the art will know that special considerations are associated with the use of antisense or cosuppression technologies in order to reduce expression of particular genes. For example, the proper level of expression of sense or antisense genes may require the use of different chimeric genes utilizing different regulatory elements known to the skilled artisan. Once transgenic plants are obtained by one of the methods described above, it will be necessary to screen individual transgenics for those that most effectively display the desired phenotype. Accordingly, the skilled artisan will develop methods for screening large numbers of transformants. The nature of these screens will generally be chosen bn practical grounds. For example, one can screen by looking for changes in gene expression by using antibodies specific for the protein encoded by the gene being suppressed, or one could establish assays that specifically measure enzyme activity. A preferred method will be one which allows large numbers of samples to be processed rapidly, since it will be expected that a large number of transformants will be negative for the desired phenotype.
In another embodiment, the present invention concerns a polypeptide of at least 351 amino acids that has at least 80% identity-based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:2, 4, 6, 8, 50, 82 and 100.
In another embodiment, the present invention concerns a polypeptide of at least 72 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:12, 16, 18, 20, 22, 24, 26 and 28.
In another embodiment, the present invention concerns a polypeptide of at least 110 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:10, 32, 36, 38, 40, 42, 44, 46, 48, 52, 60, 102, 104 and 124.
In another embodiment, the present invention concerns a polypeptide of at least 189 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:14, 34, 62, 64, 68, 70, 72, 74, 76, 78, 80, 120 and 122.
In another embodiment, the present invention concerns a polypeptide of at least 67 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:84, 86, 88, 90, 92, 94 and 96.
In another embodiment, the present invention concerns a polypeptide of at least 87 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:98, 110, 112, 114, 116 and 118.
In another embodiment, the present invention concerns a polypeptide of at least 155 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:128, 130, 132 and 134.
In another embodiment, the present invention concerns a polypeptide of at least 161 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:54, 136, 138, 140, 142 and 144.
In another embodiment, the present invention concerns a polypeptide of at least 66 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166 and 168.
In another embodiment, the present invention concerns a polypeptide of at least 141 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs:58, 106, 170, 172, 174, 176, 178, 180, 182 and 184.
In another embodiment, the present invention concerns a polypeptide of at least 81 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID:186, 188, 190, 192, 194, 196, 198, 200, 202 and 204.
In another embodiment, the present invention concerns a polypeptide of at least 48 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID:30, 56 and 108.
The instant polypeptides (or substantial portions thereof) may be produced in heterologous host cells, particularly in the cells of microbial hosts, and can be used to prepare antibodies to these proteins by methods well known to those skilled in the art. The antibodies are useful for detecting the polypeptides of the instant invention in situ in cells or in vitro in cell extracts. Preferred heterologous host cells for production of the instant polypeptides are microbial hosts. Microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign proteins are well known to those skilled in the art. Any of these could be used to construct a chimeric gene for production of the instant polypeptides. This chimeric gene could then be introduced into appropriate microorganisms via transformation to provide high level expression of the encoded metabolism protein. An example of a vector for high level expression of the instant polypeptides in a bacterial host is provided (Example 6).
All or a substantial portion of the polynucleotides of the instant invention may also be used as probes for genetically and physically mapping the genes that they are a part of, and used as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. For example, the instant nucleic acid fragments may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Maniatis) of restriction-digested plant genomic DNA may be probed with the nucleic acid fragments of the instant invention. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1:174-181) in order to construct a genetic map. In addition, the nucleic acid fragments of the instant invention may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the instant nucleic acid sequence in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J Hum. Genet. 32:314-331).
The production and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol. Reporter 4:37-41. Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.
Nucleic acid probes derived from the instant nucleic acid sequences may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al. In: Nonmammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).
In another embodiment, nucleic acid probes derived from the instant nucleic acid sequences may be used in direct fluorescence in situ hybridization (FISH) mapping (Trask (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favor use of large clones (several to several hundred KB; see Laan et al. (1995) Genome Res. 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes.
A variety of nucleic acid amplification-based methods of genetic and physical mapping may be carried out using the instant nucleic acid sequences. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med. 11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid fragment is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.
Loss of function mutant phenotypes may be identified for the instant cDNA clones either by targeted gene disruption protocols or by identifying specific mutants for these genes contained in a maize population carrying mutations in all possible genes (Ballinger and Benzer (1989) Proc. Natl. Acad. Sci USA 86:9402-9406; Koes et al. (1995) Proc. Natl. Acad. Sci USA 92:8149-8153; Bensen et al. (1995) Plant Cell 7:75-84). The latter approach may be accomplished in two ways. First, short segments of the instant nucleic acid fragments may be used in polymerase chain reaction protocols in conjunction with a mutation tag sequence primer on DNAs prepared from a population of plants in which Mutator transposons or some other mutation-causing DNA element has been introduced (see Bensen, supra). The amplification of a specific DNA fragment with these primers indicates the insertion of the mutation tag element in or near the plant gene encoding the instant polypeptides. Alternatively, the instant nucleic acid fragment may be used as a hybridization probe against PCR amplification products generated from the mutation population using the mutation tag sequence primer in conjunction with an arbitrary genomic site primer, such as that for a restriction enzyme site-anchored synthetic adaptor. With either method, a plant containing a mutation in the endogenous gene encoding the instant polypeptides can be identified and obtained. This mutant plant can then be used to determine or confirm the natural function of the instant polypeptides disclosed herein.